Fix codebase from variety of issues

[Schiano-NOAA]

Summary

Various small fixes identified from the following issues:

• BAM with plot_natural_mortality not working #156
• Error message for convert_output is inconsistent with accepted inputs #182
• [BUG]: plot_spawning_biomass grabs additional values #183
• FIMS in converter does not work when model results are directly put into converter from R environment #184
• in addition, fixed a bug in plot_spawning_biomass(...) when facet is returned from process_data(...) as character(0)

[github-actions]

New version checklist

• Package version in DESCRIPTION has been updated
• Release notes have been drafted/published
• Cheatsheet content has been updated (if applicable)
• Cheatsheet version has been updated

[github-actions]

Code Metrics Report

Coverage	Code to Test Ratio	Test Execution Time
71.2%	1:0.1	5m7s

Code coverage of files in pull request scope (66.2%)

Files	Coverage
R/convert_output.R	58.9%
R/plot_natural_mortality.R	79.6%
R/plot_spawning_biomass.R	78.9%
R/process_data.R	58.0%
R/utils_plot.R	88.2%

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Reported by octocov

[sbreitbart-NOAA]

I think everything looks good except for one thing, which I'm struggling to test: running plot_spawning_biomass() with facet. I've tried several sample datasets and faceted for fleet and sex with no luck. Can you please provide an example?

[Schiano-NOAA]

I think everything looks good except for one thing, which I'm struggling to test: running plot_spawning_biomass() with facet. I've tried several sample datasets and faceted for fleet and sex with no luck. Can you please provide an example?

Tbh I am not sure if I have any examples either

[Schiano-NOAA]

@sbreitbart-NOAA I'll do a manual test and add in try out the facet feature in spawning biomass plot

[Schiano-NOAA]

@sbreitbart-NOAA feel free to try it out, but this is how the facetting looks :) I just merged in #196 so there is a rebase

# test data
# 1. Define the dimensions
years <- 1995:2025
areas <- c(1, 2)
sexes <- c("male", "female")

# 2. Create the grid of all combinations
df <- expand.grid(year = years, area = areas, sex = sexes)

# 3. Add the static columns
df$label <- "spawning_biomass"
df$uncertainty_label <- "se"
df$module_name <- "fisheries_module_v1"

# 4. Generate synthetic values
set.seed(42)
df$estimate <- runif(nrow(df), min = 500, max = 2000)
df$uncertainty <- df$estimate * runif(nrow(df), min = 0.05, max = 0.15)

# 5. Reorder columns (including the new uncertainty_label)
df <- df[, c("label", "estimate", "uncertainty", "uncertainty_label", "module_name", "year", "area", "sex")]

# Preview the result
head(df)

devtools::load_all()

plot_spawning_biomass(df)

[sbreitbart-NOAA]

Great! This worked too: plot_spawning_biomass(df, facet = "sex"). LGTM!